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Whole‐genome duplications followed by tandem duplications drive diversification of the protein modifier SUMO in Angiosperms
Author(s) -
Hammoudi Valentin,
Vlachakis Georgios,
Schranz M. Eric,
den Burg Harrold A.
Publication year - 2016
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.13911
Subject(s) - subfunctionalization , neofunctionalization , biology , arabidopsis , gene duplication , genetics , tandem exon duplication , gene , genome , gene family , segmental duplication , mutant
Summary The ubiquitin‐like modifier ( UBL ) SUMO (Small Ubiquitin‐Like Modifier) regulates protein function. Structural rather than sequence homology typifies UBL families. However, individual UBL types, such as SUMO , show remarkable sequence conservation. Selection pressure also operates at the SUMO gene copy number, as increased SUMO levels activate immunity and alter flowering time in Arabidopsis. We show how, despite this selection pressure, the SUMO family has diversified into eight paralogues in Arabidopsis. Relationships between the paralogues were investigated using genome collinearity and gene tree analysis. We show that palaeopolyploidy followed by tandem duplications allowed expansion and then diversification of the SUMO genes. For example, Arabidopsis SUMO 5 evolved from the pan‐eudicot palaeohexaploidy event (gamma), which yielded three SUMO copies. Two gamma copies were preserved as archetype SUMO s, suggesting subfunctionalization, whereas the third copy served as a hotspot for SUMO diversification. The Brassicaceae‐specific alpha duplication then caused the duplication of one archetype gamma copy, which, by subfunctionalization, allowed the retention of both SUMO 1 and SUMO 2 . The other archetype gamma copy was simultaneously pseudogenized ( SUMO 4/6 ). A tandem duplication of SUMO 2 subsequently yielded SUMO 3 in the Brassicaceae crown group. SUMO 3 potentially neofunctionalized in Arabidopsis, but it is lost in many Brassicaceae. Our advanced methodology allows the study of the birth and fixation of other paralogues in plants.